Link to this post | posted 09 Mar, 2022 15:56
afreise	Update: I've generated the files successfully! I think now I just need to pare down in excel to the only phages I want to compare. Right now gene.csv has all 4000+ phages and genes and I think my computer will explode if I run the GCS script on all of them. Even though I've only listed my subset of AZ phages in genome.csv, I should still need to pare down gene.csv to those phages too, right?

Link to this post | posted 09 Mar, 2022 01:04

afreise

Hello, I am attempting to do a large-scale GCS comparison of all the phages in Cluster AZ (and plan to do this on other phages as well in the future). My former TA Andrew Kapinos wrote up a set of instructions to accompany the github code for the Pope & Mavrich 2017 batch GCS/MaxGCDGap scripts. I've been able to set up mySQL and other necessary components, and successfully pulled some data, but am stuck again. When I do the data pull from the Actino_Draft database using mySQL, I can't seem to pull the pham and function data that the GCS scripts require for the function.csv file, according to the instructions I have (I left comments in that file to highlight where I got stuck). Can anyone make a recommendation of what I might try next? Kudos to Nick for the help he's provided so far - thought I'd ask here as well so I'm not pestering him too much! (thanks Nick!) Best, Amanda

Link to this post | posted 18 Feb, 2022 16:21
afreise	Awesome! Thank you Christian. I will download the new one and email you with any questions I have.

Link to this post | posted 17 Feb, 2022 23:31

afreise

Hi all, I've followed the directions above in the SEA VM to try to install Phamnexus. It appears to have been cloned and installed, but when I click on PhamNexus, nothing happens… Not sure if it makes a difference, but I am using the version of the SEAVM downloaded here (https://seaphages.org/software/virtualmachine/) just a few weeks ago. I've attached a screenshot of the VM environment. Any advice is most welcome! - (As a second issue, I also tried the above trick to "Check for Updates" in the working version of PhamNexus we have installed on our computer lab computers, and the database did not update. Any recommendations for that would also be very helpful.) 400Kb

Link to this post | posted 11 Feb, 2022 02:37
afreise	My guess is that Starterator just doesn't have the capability to say "there's a tie." It probably just chose the first of the two starts and designated that as the most-annotated one even though they are actually equal.

Link to this post | posted 17 Nov, 2021 00:04
afreise	Thank you for the question Arturo and the answer Debbie - we had the same question for our Cluster DE phage ObLaDi. Much appreciated!

Link to this post | posted 12 Nov, 2021 16:18

afreise

Hi all, thank you so much for this information! Like Kyle, I have several students interested in doing independent research projects, so I was considering having them pilot/optimize/test these hosts first to see if we are able to use them for PHAGES in the future. It would be great to meet and chat about good options for new hosts. Vic, I will send you an email. I'll CC you as well Kyle. Best, Amanda

Link to this post | posted 11 Nov, 2021 22:51
afreise	Thanks Kyle! Good to know.

Link to this post | posted 11 Nov, 2021 00:43

afreise

Hi everyone, In 2022 I will be developing a new CURE at UCLA focusing on analysis of the human microbiome. I'd like to align it with our Phage Hunters class, and try some hosts that have some relevance. Before I dive in, just wanted to see if anyone has any thoughts or experience with the following hosts: -Corynebacterium is my plan A right now since we've already had numerous phages isolated on this host. -We're also thinking of trying to isolate from oral samples on Rothia dentocariosa. I noticed there are just a couple of phages for this one; from a quick lit search it seems like it might be a rare microbe, at least in healthy mouths? Maybe we can get some samples donated from the UCLA dental school… -I noticed a couple of new hosts, Kocuria kristinae and Dietzia maris, on the Hosts page. They haven't had more than a couple phages isolated on them yet. Is this a potential/good option? (Wondering if they haven't had phages isolated yet because they are difficult to work with… Also, I'd be interested to hear if anyone at SEA-PHAGES HQ has priority hosts they'd like new phages on. Thanks in advance for any thoughts! Amanda

Link to this post | posted 15 Oct, 2021 01:24
afreise	Thank you both very much!